and uploaded a source distribution to the google code site:
https://rdkit.googlecode.com/files/RDKit_2013_03_1beta1.tgz
There's still some documentation work to do, but I wanted to get the
changes out there for the community to test.
If no show-stopper bugs appear, I will do the release itself at the
end of next week.
Excerpts from the updated release notes are below.
Best Regards,
-greg
****** Release_2013.03.1 *******
(Changes relative to Release_2012.12.1)
!!!!!! IMPORTANT !!!!!!
- The algorithm for hashing subgraphs used in the RDKit fingerprinter
has changed. The new default behavior will return different
fingerprints than previous RDKit versions. This affects usage from
c++, python, and within the postgresql cartridge. See the "Other"
section below for more details.
Acknowledgements:
Jan Domanski, Jean-Paul Ebejer, Nikolas Fechner, Jameed Hussain,
Stephan Reiling, Sereina Riniker, Roger Sayle
Bug Fixes:
- removeBond now updates bond indices (sf.net issue 284)
- dummy labels are no longer lost when atoms are copied (sf.net issue
285)
- more specific BRICS queries now match before less specific ones
(sf.net issue 287, github issue 1)
- molAtomMapNumber can now be set from Python (sf.net issue 288)
- the legend centering for molecular image grids has been improved
(sf.net issue 289)
- make install now includes all headers (github issue 2)
- InChIs generaged after clearing computed properties are now correct
(github issue 3)
- Reacting atoms that don't change connectivity no longer lose
stereochemistry (github issue 4)
- Aromatic Si is now accepted (github issue 5)
- removeAtom (and deleteSubstructs) now correctly updates stereoAtoms
(github issue 8)
- [cartridge] pg_dump no longer fails when molecules cannot be
converted to SMILES (github issue 9)
- a canonicalization bug in MolFragmentToSmiles was fixed (github issue 12)
- atom labels at the edge of the drawing are no longer cut off
(github issue 13)
- a bug in query-atom -- query-atom matching was fixed (github issue 15)
- calling ChemicalReaction.RunReactants from Python with None
molecules no longer leads to a seg fault. (github issue 16)
- AllChem.ReactionFromSmarts now generates an error message when called
with an empty string.
- Writing CTABs now includes information about atom aliases.
- An error in the example fdef file
$RDBASE/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef
has been fixed. (github issue 17)
- Quantize.FindVarMultQuantBounds() no longer generates a seg fault
when called with bad arguments. (github issue 18)
New Features:
- The handling of chirality in reactions has been reworked and
improved. Please see the RDKit Book for an explanation.
- Atom-pair and topological-torsion fingerprints now support the
inclusion of chirality in the atom invariants.
- A number of new compositional descriptors have been added:
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
- An implementation of the molecular quantum number (MQN) descriptors
has been added.
- RDKFingerprintMol now takes an optional atomBits argument which is
used to return information about which bits atoms are involved in.
- LayeredFingerprintMol no longer takes the arguments tgtDensity and
minSize. They were not being used.
- LayeredFingerprintMol2 has been renamed to PatternFingerprintMol
- The substructure matcher can now properly take stereochemistry into
account if the useChirality flag is provided.
- The module rdkit.Chem.Draw.mplCanvas has been added back to svn.
New Database Cartridge Features:
- The new compositional descriptors are available:
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
- MACCS fingerprints are available
- the substruct_count function is now available
- substructure indexing has improved
New Java Wrapper Features:
- The new compositional descriptors are available:
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
- The molecular quantum number (MQN) descriptors are available
- MACCS fingerprints are available
- BRICS decomposition is available.
Deprecated modules (to be removed in next release):
Removed modules:
Other:
- RDKit fingerprint generation is now faster. The hashing algorithm
used in the RDKit fingerprinter has changed.
- Force-field calculations are substantially faster (sf.net issue 290)
- The core of the BRICS implementation has been moved into C++.
- The MACCS fingerprint implementation has been moved into
C++. (contribution from Roger Sayle)
- New documentation has been added: Cartridge.rst, Overview.rst,
Install.rst
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